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2,868 results for “variant”
Inbred Strain Variant Database (ISVdb): A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders
<p>Data files for the development of a database for storing (and a GUI for retrieving) the imputed variants for 72 Collaborative Cross strains of mice. Files include the inputs for the imputation, as well as the final results. See File_S1_Readme for more details on the included files.</p>
Native MS dataset for: "Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants"
<p>Native mass spectrometry dataset used in: <strong>Insights into the pathogenesis of primary hyperoxaluria type I from the structural dynamics of alanine:glyoxylate aminotransferase variants.</strong> Pavla Vankova, Juan Luis Pacheco-Garcia, Dmitry S. Loginov, Atanasio Gómez-Mulas, Alan Kádek, José Manuel Martín-Garcia, Eduardo Salido, Petr Man and Angel L. Pey. FEBS Letters (2024)</p> <p><strong>Description:</strong></p> <p>Native mass spectrometry (MS) analysis verifying the oligomeric state of alanine:glyoxylate aminotransferase (AGT) protein and its P11L and I340M (LM) polymorphism and LM G170R mutation variants in primary hyperoxaluria type I.</p> <p><strong>Sample processing:</strong></p> <p>AGT protein as well as its LM and LM G130R mutants were buffer exchanged into 150 mM aqueous ammonium acetate solution (pH 7.5, MS-grade, Sigma-Aldrich) through six cycles of tenfold dilution and re-concentration using centrifugal concentrators Vivaspin 500 (30 kDa cut-off, <em>Sartorius</em>). Desalted proteins were introduced into a Synapt G2Si mass spectrometer (Waters) via static nanoelectrospray ionization from in-house prepared gold-coated borosilicate glass capillaries Kwik-Fil 1B120F-4 (<em>World Precision Instruments</em>). Protein concentration in samples was determined by 280 nm absorbance measurements using DeNovix DS-11 spectrophotometer. Samples were diluted in ammonium acetate and electrosprayed at 1 and 2 µM concentration. The mass spectrometer was carefully tuned for best signal quality and intensity, while keeping ion activation and unfolding minimal. Namely, electrospray voltage was kept at 1.3 kV, source desolvation temperature 80°C, sampling cone 80 V and 10 V collision voltage with 6 ml/min flow of argon in the trap region for thermalization of ions. Quadrupole was operated in a broadband transmission mode up to 8000 m/z while the spectra were acquired in mass range 500 – 20000 m/z. Spectra were externally mass recalibrated using known masses of caesium iodide clusters.</p> <p><strong>Data processing:</strong></p> <p>Raw mass spectra were averaged over 75 scans and further processed in Waters MassLynx 4.1. The averaged spectra were exported for ZENODO deposition as plain in plain m/z vs intensity .txt files as well uploaded as part of the .raw file format of the whole analysis (including initial metadata) with scan descriptions and parameter changes described in a stand-alone .txt descriptor file.</p>
Fastq files for benchmarking somatic variant calling pipelines
<p>The <a href="https://download.imgag.de/public/validation_dataset_somatic/readme.html" target="_blank" rel="noopener">original .bam files</a> were provided by <a href="https://www.medizin.uni-tuebingen.de/de/das-klinikum/mitarbeiter/profil/3377" target="_blank" rel="noopener">Marc Sturm</a> from the <a href="https://www.medizin.uni-tuebingen.de/de/das-klinikum/einrichtungen/institute/medizinische-genetik-und-angewandte-genomik" target="_blank" rel="noopener">Institut für Medizinische Genetik und Angewandte Genomik at the University Clinic Tübingen.</a></p> <p>The files were transformed into .fq.gz files using the <a href="https://github.com/nf-core/bamtofastq" target="_blank" rel="noopener">nf-core/bamtofastq pipeline.</a> All information on the pipeline run can be found in the <a href="../api/records/10805134/draft/files/execution_report_2024-03-11_11-44-17.html/content" target="_blank" rel="noopener noreferrer">execution_report_2024-03-11_11-44-17.html</a>. The FASTQ files for the normal sample were directly uploaded to <a href="https://osf.io/cduyq/files/onedrive">the corresponding osf project</a>.</p> <p> </p> <p> </p>
Research Data for Comparative Evaluation of RT-PCR and Antigen-based Rapid Diagnostic Tests (Ag-RDTs) for SARS-CoV-2 Detection: Performance, Variant Specificity, and Clinical Implications
<p>This dataset represents laboratory findings for the comparative evaluation of the diagnostic performance of Ag-RDTs (Flourescence Immunoassay and Lateral Flow Immunoassay) with RT-PCR</p>
ADIPOQ Gene Variants (rs266729, rs2241766, rs1501299) and Acute Myocardial Infarction in Vietnamese Patients with Type 2 Diabetes Mellitus
<p>This data is from a study project about ADIPOQ Gene Variants (rs266729, rs2241766, rs1501299) and Acute Myocardial Infarction in Vietnamese Patients with Type 2 Diabetes Mellitus. The data contains information from 550 patients with their identification removed to ensure confidentiality.</p>
BAM reference data: Temperature-dependent Young's and shear modulus data for additively and conventionally manufactured variants of Ni-based alloy Inconel IN718
<p>This BAM reference dataset reports the elastic properties (Young's modulus, shear modulus) of Ni-based alloy Inconel IN718 between room temperature and 800 °C in an additively manufactured variant (laser powder bed fusion, PBF‑LB/M) and from a conventional process route (hot rolled bar). It was generated in an accredited test laboratory using calibrated measuring equipment. The calibrations meet the requirements of the test procedure and are metrologically traceable. The dataset was audited as BAM reference data.</p>
BAM reference data: Temperature-dependent Young's and shear modulus data for additively and conventionally manufactured variants of Ti-6Al-4V
<p>This BAM reference dataset reports the elastic properties (Young's modulus, shear modulus) of titanium alloy Ti-6Al-4V between room temperature and 400 °C in an additively manufactured variant (laser-based directed energy deposition with powder as feedstock, DED-LB/M) and from a conventional process route (hot rolled bar). It was generated in an accredited test laboratory using calibrated measuring equipment. The calibrations meet the requirements of the test procedure and are metrologically traceable. The dataset was audited as BAM reference data.</p>
BAM reference data: Temperature-dependent Young's and shear modulus data for additively and conventionally manufactured variants of austenitic stainless steel AISI 316L
<p><span>This BAM reference dataset reports the elastic properties (Young's modulus, shear modulus) of austenitic stainless steel AISI 316L between room temperature and 900 °C in an additively manufactured variant (laser powder bed fusion, PBF</span><span>‑</span><span>LB/M) and from a conventional process route (hot rolled sheet). It was generated in an accredited test laboratory using calibrated measuring equipment. The calibrations meet the requirements of the test procedure and are metrologically traceable. The dataset was audited as BAM reference data.</span></p>
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
<p>The below data are associated with our paper entitled "Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance."</p> <p>1) SNP-gene link predictions generated by pgBoost and existing methods SCENT (Sakaue et al. 2024 <em>Nat Genet</em>), Signac (Stuart et al. 2021 <em>Nat Methods</em>), ArchR (Granja et al. 2021 <em>Nat Genet</em>), and Cicero (Pliner et al. 2018 <em>Mol Cell</em>).</p> <p><strong>pgBoost_scores.tsv.gz </strong>contains linking predictions made by pgBoost.</p> <p><strong>constituent_method_scores.tsv.gz</strong> contains linking predictions made by constituent methods.</p> <p><em><span>**NOTE: promoters (+/- 1kb from TSS) and candidate links >500kb are excluded from linking predictions (see manuscript)**</span></em></p> <p>Linking scores and percentiles are reported for each method (pgBoost score, SCENT FDR, Signac correlation, ArchR correlation, Cicero co-accessibility). Rank percentiles are computed as: 1 - (rank / n). When multiple links receive the same score, they are assigned the percentile of the top rank. Links unscored by each method (denoted by zeros* in the linking score column) are assigned a percentile equivalent to the percent of links unscored by the focal method. See the Methods section of the paper for further details on computing linking scores and summarizing scores across cell types and data sets.</p> <p>*Candidate links tested and assigned a co-accessibility of zero by the Cicero method are given a score of 1e-100 in the "Cicero" column to distinguish between unscored candidate links and candidate links assigned a partial correlation of zero (see Pliner et al. 2018 <em>Mol Cell</em>).</p> <p><em>NOTE: The predictions associated with this release (version 2) were generated using an expanded set of data sets, an expanded training set, and corrected TSS coordinates.</em></p> <p>2) GWAS-derived evaluation SNP-gene link evaluation set.</p> <p><strong>gwas_evaluation.tsv</strong>: GWAS-derived evaluation SNP-gene link evaluation set. Column 1 provides SNP coordinates in the format <chr-start-end>. This evaluation framework was proposed by Weeks et al. 2024 <em>Nature Genetics</em> based on fine-mapping results from Kanai et al. <em>medrxiv</em> (see Methods: <em>Evaluation data sets</em> of Dorans et al.). "True" links (gold = 1) are non-coding variants fine-mapped to a focal trait (PIP > 0.1) with a coding variant for exactly one candidate gene within 1 Mb attaining PIP > 0.5 for the same trait. "False" links (gold = 0) are candidate SNP-gene pairs involving a SNP with a "true" link. This file of SNP-gene links was adapted from credible set-gene links <a href="https://github.com/Deylab999/GWAS_benchmark_IGVF/blob/bb91d08cc02d59cdd829eb1430569057ac26c5fe/V2G/ENCODE_E2G_2023/UKBiobank.ABCGene.anyabc.tsv">here</a> (the "truth" column defines true/false links) by identifying SNPs with PIP > 0.1 within each credible set-gene link.</p>
Data files and videos for manuscript "Biallelic pathogenic variants in ROBO1 associate with syndromic CAKUT"
<p>#2021-11-20<br> #Summary<br> This ZIP-file contains the supplementary files of our ROBO1 study. <br> Suppl. File S1 details the next-generation sequencing-based gene panel comprising 426 CKD-associated genes performed in ID 1.<br> Suppl. File S2 contains a variant information and raw in silico data.<br> Suppl. Videos SV1A and SV1B show cardiac valve anomalies comprising mitral valve prolapse in ID 1.<br> Suppl. Video SV2 shows renal anomalies and hydroureter as documented in-vivo by microCT-scan of the mutant mice.</p> <p>#Folder structure<br> ./ (parent directory containing this README file and all subfolders)<br> ./Files/ (contains Excel Suppl. File S1 and Suppl.File S2)<br> ./Videos/ (contains the Suppl. Videos)</p> <p><br> #Files and checksums<br> Algorithm Hash Path<br> --------- ---- ----<br> MD5 2BCB0774F8303FC5DBA2313DFD19FBEE Files\FileS1_Panel-Content.xlsx<br> MD5 015F01832AE1C6610D9C1FB8902FDF17 Files\FileS2_Variants-and-Domains_2021-05-18.xlsx<br> MD5 8BBE3DE1C21F161BCE07A2AFB4A6F7CD Videos\Supplementary Video SV1\Supplementary Video SV1.docx<br> MD5 5EA354253D7E489B48EDFBDE59CFB798 Videos\Supplementary Video SV1\Supplementary Video SV1A.mov<br> MD5 61796C4A5F7EAD79D642ED9D11514A95 Videos\Supplementary Video SV1\Supplementary Video SV1B.mov<br> MD5 4098A23D5CE1C67C1D507D4DD5F4F866 Videos\Supplementary Video SV2\Lo_Robo mutant.mov<br> MD5 D0B219332F227DBECF1A2A1A6AD0925A Videos\Supplementary Video SV2\Supplementary Video SV2.mov</p>
Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants.
<p>Datasets: <em>CommonClinvar</em> and <em>NewClinvar</em></p> <p>Authors: Emidio Capriotti and Piero Fariselli</p> <p>Article: Evaluating the relevance of sequence conservation in the prediction of pathogenic missense variants.<br> </p>
Summary statistics for association tests between human and Plasmodium falciparum genetic variants in 3,346 severe malaria cases from The Gambia and Kenya
<p>This dataset contains summary statistics for association tests between human and<br> <em>Plasmodium falciparum</em> malaria parasite genetic variants, using data from 3,346 severe malaria cases from The Gambia and Kenya. These results underlie the analysis described in our paper:</p> <p><strong>"Malaria protection due to sickle haemoglobin depends on parasite genotype"</strong></p> <p>Gavin Band, Ellen M. Leffler, Muminatou Jallow, Fatoumatta Sisay-Joof, Carolyne M. Ndila, Alexander W. Macharia, Christina Hubbart, Anna E. Jeffreys, Kate Rowlands, Thuy Nguyen, Sónia M. Gonçalves, Cristina V. Ariani, Jim Stalker, Richard D. Pearson, Roberto Amato, Eleanor Drury, Giorgio Sirugo, Umberto d'Alessandro, Kalifa A. Bojang, Kevin Marsh, Norbert Peshu, Joseph W. Saelens, Mahamadou Diakité, Steve M. Taylor, David J. Conway, Thomas N. Williams, Kirk A. Rockett, Dominic P. Kwiatkowski</p> <p>Nature (2021) doi: <a href="https://doi.org/10.1038/s41586-021-04288-3">10.1038/s41586-021-04288-3</a> <strong>bioRxiv link</strong>:: <a href="https://doi.org/10.1101/2021.03.30.437659">doi.org/10.1101/2021.03.30.437659</a><br> <br> The genotype data underlying these summary statistics has also been deposited on Zenodo<br> (<a href="https://zenodo.org/record/4973477">doi:10.5281/zenodo.4973477</a>). The <a href="https://www.well.ox.ac.uk/~gav/hptest)">HPTEST software</a> used to generate these results has also been deposited (<a href="https://doi.org/10.5281/zenodo.5685580">doi:10.5281/zenodo.5685580</a>). Please see the <a href="https://www.malariagen.net/resource/32">MalariaGEN website</a> for a full list of datasets which have been released with this manuscript.</p> <p><strong>Data contents.</strong></p> <p>The dataset consists of a single <a href="http://sqlite.org">sqlite database file</a> containing the results, and an accompanying README file in markdown and html format. Please see the README file for full details of the data contents.</p> <p> </p>
Predictions of the SARS-CoV-2 B.1.1.529 Variant Spike Protein Receptor Binding Domain Structure and Neutralizing Antibody Interactions
<p>Using AlphaFold2 and HADDOCK, we have generated a predicted structure for the SARS-CoV-2 B.1.1.529 variant's Spike receptor binding domain and then predicted the binding interaction with neutralizing antibodies. This was performed to understand the potential structural changes in the receptor binding domain of B.1.1.529 and how this may affect vaccine efficacy through antibody interaction.</p>
Supplementary material for: "Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations"
<p>Supplementary material for the publication "Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations"</p> <p>The realated preprint can be found at Research Square (<a href="https://doi.org/10.21203/rs.3.rs-861830/v1">https://doi.org/10.21203/rs.3.rs-861830/v1</a>)</p> <p>Supplementary file 1: Supplementary results, tables and figures.</p> <p>Supplementary file 2: MultiQC report.</p> <p>Supplementary file 3: Observer concordance of the visual filtering step.</p> <p>Supplementary file 4: Snakemake workflow and scripts.</p> <p> </p>
Supplemental Material Surveillance Improves Outcomes for Carriers of SDHB Pathogenic Variants
<p><strong>Supplemental table for Surveillance improves outcomes for carriers of <em>SDHB</em> pathogenic variants: a multi-center study</strong></p>
Variant Forks -- Motivations and Impediments
<p>Social coding platforms centred around git provide explicit facilities to share code between projects: forks, pull requests, cherry-picking to name but a few. Variant forks are an interesting phenomenon in that respect, as it permits for different projects to peacefully co-exist, yet explicitly acknowledge the common ancestry. Several researchers analysed forking practices on open source platforms and observed that variant forks get created frequently. However, today little is known on the motivations for launching such a variant fork. Is it mainly technical (e.g., diverging features), governance (e.g., diverging interests), legal (e.g., diverging licences), or do other factors come into play? In this paper we report the results of an exploratory qualitative analysis on the motivations behind variants creation and maintenance. We surveyed 105 maintainers of different active open source variant projects hosted on GitHub. Our study extends previous findings, identifying a number of fine-grained common motivations for launching a variant fork and listing concrete impediments for maintaining the co-existing projects.</p>
Immune disease variants modulate gene expression in regulatory CD4+ T cells
<p>We mapped genetic regulation (QTL) of gene expression and chromatin activity in Tregs and we identified 133 colocalizing loci with immune disease variants.<br> For the time being, the preprint DOI: <a href="https://doi.org/10.1101/654632">10.1101/654632</a></p>
Supplementary files for, 'Developmental morphology and anatomy shed light on both parallel and convergent evolution of the umbellate inflorescence in Monocots, underlied by a new variant of metatopy.'
<p>Supplementary file for forth coming manuscript. Consists of Pre-processed microscopy images, FiJI readable annotated stacks and raw laser ablation tomography video data</p> <p> </p> <p><strong>File name: </strong>MainFigures.zip </p> <p><strong>File format:</strong> .zip, individual images in .bmp format.</p> <p><strong>Description of data:</strong> Picolay output of main figure panels.</p> <p> </p> <p><strong>File name: </strong>Supplementary_File_1</p> <p><strong>File format:</strong> .MOV (video)</p> <p><strong>Description of data:</strong> Movie 1 LAT scan of <em>Butomus umbellatus</em></p> <p> </p> <p><strong>File name: </strong>Supplementary_File_2</p> <p><strong>File format:</strong> .AVI (video)</p> <p><strong>Description of data:</strong> Three-dimensional reconstruction of <em>Butomus umbellatus</em> inflorescence</p> <p> </p> <p><strong>File name: </strong>Supplementary_File_3</p> <p><strong>File format:</strong> .MOV (video)</p> <p><strong>Description of data:</strong> Movie 3 Three-dimensional reconstruction of <em>Butomus umbellatus</em> vasculature</p> <p> </p> <p><strong>File name: </strong>Supplementary_File_4</p> <p><strong>File format:</strong> .TIFF (Can be opened in FIJI)</p> <p><strong>Description of data:</strong> <em>Butomus</em> <em>umbellatus </em>vasculature composite tiff file</p> <p> </p> <p><strong>File name: </strong>Supplementary_File_5</p> <p><strong>File format:</strong> .MOV (video)</p> <p><strong>Description of data:</strong> LAT scan of O<em>rnithogalum umbellatum</em></p> <p> </p> <p><strong>File name: </strong>Supplementary_File_6</p> <p><strong>File format:</strong> .TIFF (Can be opened in FIJI)</p> <p><strong>Description of data:</strong> <em>Ornithogalum umbellatum</em> vasculature tiff file (Can be opened in FIJI)</p> <p> </p> <p><strong>File name: </strong>Supplementary_File_7</p> <p><strong>File format:</strong> .MOV (video)</p> <p><strong>Description of data:</strong> LAT scan of <em>Allium hollandicum</em> inflorescence</p>
Data files for manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2"
<p>#2022-02-21<br> #Summary<br> This ZIP-file contains the data files used for all analyses for the manuscript "A novel syndrome caused by the constitutional gain-of-function variant p.Glu1099Lys in NSD2".</p> <p><br> #File structure<br> README.txt This README file.<br> File S02 ("FileS02_NSD2-clinical-information-and-variants.xlsx") Clinical data of GoF and LoF inidviduals used for Table 1 and Table 2 and genetic variant data used for Figure 2.<br> File S03 ("FileS03_NSD2-CCLE-analyses.xlsx") Tables containing information of the CCLE analyses and depmap results used for Figure 3A-D.<br> File S04 ("FileS04_humanbase_global_1642958821189.tar.gz") Tar.gz file of the downlaoded humanbase result files used for Figure 3E.</p> <p><br> #Files and checksums<br> 5FE613FC7646419C20153068E8D5F463 ./FileS02_NSD2-clinical-information-and-variants.xlsx<br> AC53634E6044469BE42DBBE8F7503275 ./FileS03_NSD2-CCLE-analyses.xlsx<br> 7AE58A28A4D1E1462521A37522BB78B6 ./FileS04_humanbase_global_1642958821189.tar.gz</p>
Local adaptation and archaic introgression shape global diversity at human structural variant loci
<p>Supporting data associated with the manuscript "Local adaptation and archaic introgression shape global diversity at human structural variant loci". These include:</p> <ul> <li>structural variant genotypes (Paragraph; <a href="https://github.com/Illumina/paragraph">https://github.com/Illumina/paragraph</a>)</li> <li>eQTL mapping results (fastqtl permutation pass; see <a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a> for column descriptions)</li> <li>eQTL fine-mapping results (CAVIAR; see <a href="http://genetics.cs.ucla.edu/caviar/index.html">http://genetics.cs.ucla.edu/caviar/index.html</a>)</li> <li>structural variant selection scan results (Ohana; <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</li> </ul> <p>Description of files in this directory:</p> <p><strong>Structural variant genotypes</strong></p> <p><code>SVs_paragraphFormat.vcf.gz</code> - merged long-read structural variant calls</p> <p><code>SVs_1KGP_pgGTs.vcf.gz</code> - genotypes for 1000 Genomes samples in VCF format</p> <p><strong>eQTL mapping results</strong></p> <p><code>fastqtl_out.txt</code> - results from fastQTL permutation pass; see <a href="http://fastqtl.sourceforge.net/">http://fastqtl.sourceforge.net/</a> for column descriptions</p> <p><code>caviar_out.txt</code> - results from fine-mapping SNPs and SVs at significant SV eQTL loci with CAVIAR. Description of columns:</p> <ul> <li>query_sv: SV that was a significant eQTL and underwent fine-mapping</li> <li>gene_id: gene exhibiting an expression association with the query_sv</li> <li>var_id: variant (SNV or SV) that was tested for expression association with the above gene in the fine-mapping analysis</li> <li>var_in_credible_causal_set: Boolean variable denoting whether the above variant is in the 95% credible causal set</li> <li>prob_in_pcausal_set: the amount that this variant contributes to 95% credible causal set</li> <li>causal_post_prob: the posterior probability that the variant is causal in the expression association</li> </ul> <p><strong>Structural variant selection scan results</strong></p> <p><code>chr21_pruned_50_Q.matrix</code> - admixture proportion matrix (generated by Ohana; <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</p> <p><code>chr21_pruned_50_F.matrix</code> - matrix of inferred ancestral allele frequencies (generated by Ohana)</p> <p><code>chr21_pruned_50_C.matrix</code> - matrix of ancestry component covariances (generated by Ohana) Entries of the matrix can be modified to produce "selection hypothesis" matrices where allele frequencies are allowed to vary in one ancestry component (<a href="https://github.com/jade-cheng/ohana/wiki/Population-or-ancestry-specific-selection-scan">https://github.com/jade-cheng/ohana/wiki/Population-or-ancestry-specific-selection-scan</a>).</p> <p><code>selscan_50_k8_p*.txt.gz</code> - raw output of Ohana selscan (see <a href="https://github.com/jade-cheng/ohana">https://github.com/jade-cheng/ohana</a>)</p> <p><code>selscan_res.txt.gz</code> - Ohana selection scan results. These results have been filtered to exclude SVs that have low genotyping rates (<50% of samples), violate Hardy-Weinberg equilibrium expectations (excess of heterozygotes) in more than half of populations, or have extreme global log likelihood estimate (LLE) values. Description of columns:</p> <ul> <li>ID: SV ID</li> <li>#CHROM: SV chromosome</li> <li>POS: SV start position</li> <li>SVLEN: SV length (negative for deletions)</li> <li>step: number of steps needed to interpolate between genome-wide and selection hypothesis models</li> <li>lle_ratio: likelihood ratio statistic (LRS) of the genome-wide vs. selection hypothesis model</li> <li>global-lle: log likelihood of the genome-wide model</li> <li>local-lle: log likelihood of the selection hypothesis model</li> <li>f-pop0: inferred allele frequency in ancestry component 0</li> <li>f-pop1: inferred allele frequency in ancestry component 1</li> <li>f-pop2: inferred allele frequency in ancestry component 2</li> <li>f-pop3: inferred allele frequency in ancestry component 3</li> <li>f-pop4: inferred allele frequency in ancestry component 4</li> <li>f-pop5: inferred allele frequency in ancestry component 5</li> <li>f-pop6: inferred allele frequency in ancestry component 6</li> <li>f-pop7: inferred allele frequency in ancestry component 7</li> <li>ancestry_component: ancestry component tested by the selection hypothesis model. Note that we have added 1 to the ancestry component numbers to match the terminology used in paper (which orders the components from 1-8 rather than 0-7 for interpretability)</li> <li>snp_perc: SV's percentile in the LRS distribution for frequency-matched SNPs</li> <li>p_nominal: nominal p-value calculated from the likelihood ratio</li> <li>p_adj: adjusted p-value calculated from the likelihood ratio</li> </ul> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.